scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- feat: add WNN
- Integration Testing CI Install Failure on python 3.12
- perf: numba kernels for pp.harmony_integrate
- fix: symmetric gauss connectivities for pynndescent / sparse distances
- `neighbors(method="gauss")` returns a non-symmetric connectivity matrix on the sparse (pynndescent / transformer) path
- feat: `sc.tl.markers` and `sc.pp.de.deseq2`
- perf: avoid dense BasePlot aggregation
- Multi-column `groupby` crashes on non-string observations in dotplot/matrixplot/heatmap
- fix: honor user-supplied hue in sc.pl.violin
- fix: multi-column groupby crashing on non-string observations
- Docs
- Python not yet supported